I want to save a backup of my data on a remote server, but never want the backup server to see the data unencrypted. Editing a single file and backing up should not result in everything being encrypted and sent again. The remote server should preferably not even know the directory structure (and especially not the directory names).

Use rsyncrypto to encrypt files from your plaintext directory to your encrypted directory, and decrypt files from your encrypted directory and your plaintext directory, using keys that you keep locally.

Use rsync to synchronize between your encrypted directory and the remote host.

The rsyncrypto implementation you can download now from Sourceforge not only handles changes in bytes, but also insertions and deletions.

With rsyncrypto, all encryption keys never leave the local computer.

"The remote server should preferably not even know the directory structure"

In that case, you'll want to use the --name-encrypt=map option.
That makes each encrypted file name is a random string of characters,
and by default all mangled file names are stored in a single directory.
The true file names and folder names are stored in the (encrypted) file named "filemap".